Abstract: 【Objective】 The distribution characteristics of SSR sequence of the Medicago polymorpha genome were analyzed and compared with the main species of Medicago， in order to provide theoretical basis for the development of SSR molecular markers in Medicago polymorpha. 【Method】 MISA software was used to search the high-quality genome of Medicago polymorpha， Medicago truncatula and Medicago sativa， and then the SSR sequence distribution characteristics were compared and analyzed. 【Result】 In the genome of Medicago polymorpha， Medicago truncatula and Medicago sativa， 195，753， 242，434 and 390，496 complete SSR sequences were screened， with relative densities of 428 /Mb， 564 /Mb and 478 /Mb， respectively. Total length of SSR sequences were 3，611，698 bp， 3，657，503 bp and 6，307，211 bp accounted for 0.79%， 0.85% and 0.77% of the total genome sequence length respectively. Among the 1~6 different nucleotide repeat units， the single nucleotide repeat units were the most in Medicago polymorpha and Medicago truncatula， followed by dinucleotide， trinucleotide， tetranucleotide， pentanucleotide and hexanucleotide repeat units， while the hexanucleotide repeat units were more than pentanucleotide repeat units in Medicago sativa. A， T， AT， TA， AG and TC were common repeat unit types among the three alfalfa species， and the proportion of SSR with low fragment length in Medicago polymorphagenome was higher than that in Medicago truncatula and Medicago sativa. 【Conclusion】 The SSR distribution densityin the genome of Medicago polymorpha was lower than that of Medicago truncatula and Medicago sativa. SSR repeat unit types in Medicago polymorphagenomeare abundant and have great potential for developing polymorphic markers， which has important application value in the genetic diversity and molecular marker-assisted breeding of Medicago polymorpha.